There are 3 general store locations in boston. If you look at your map in game you should see the "£" symbol.. which in game has much straighter lines. These are the stores.
First one is north edge of the map, near the middle as far as east/west orientation goes.
Second one is closer to the middle of the whole map, but a little east. It's just southwest of the giant pier/dock.
Third one is directly south of the second about halfway to the entrance of the frontier. It's about a block east of the hilly area of boston... if you follow the main road from the stone gate on the south end of the city and keep on your right you will eventually find it.